Publications

Journal Articles

  • Testa A, Oliver RP, Hane JK (2015) Overview of genomic and bioinformatic resources for Zymoseptoria tritici. Fungal Genetics & Biology 79, 13–16
  • McDonald MC, Williams AH, Milgate A, Pattemore JA, Solomon PS, Hane JK (2015) Next-generation re-sequencing as a tool for rapid bioinformatic screening of presence and absence of genes and accessory chromosomes across isolates of Zymoseptoria tritici. Fungal Genetics & Biology 79, 71–75
  • Thatcher LF, Kamphuis LG, Hane JK, Singh KB, ESR1 is a mediator of transcriptional responses to biotic and abiotic stress. (2015) PLoS ONE 10 (5), e0126978
  • Foley RC, Jimenez-Lopez JC, Kamphuis LG, Hane JK, Singh KB (2015) Comparative genomic study of conglutin families across lupin species. BMC Plant Biology 15:106
  • Testa AC, Hane JK, Ellwood SR, Oliver RP (2015) CodingQuarry: Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts. BMC Genomics 16 (1), 170
  • Kamphuis LG, Hane JK, Nelson MN, Gao L, Atkins CA, Singh KB (2015) Transcriptome sequencing of different narrow‐leafed lupin tissue types provides a comprehensive uni‐gene assembly and extensive gene‐based molecular markers. Plant Biotechnology Journal 13(1):14-25
  • Hane JK, Anderson JP, Williams AH, Sperschneider J, Singh KB (2014) Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8. PLOS Genetics 10(5):e1004281
  • Pattemore JA, Hane JK, Williams AH, Wilson BAL, Stodart BJ, Ash GJ (2014) The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species. BMC Genomics 15(1):660
  • Wang A, Pattemore J, Ash G, Williams A, Hane J (2013) Draft genome sequence of Bacillus thuringiensis strain DAR 81934, which exhibits molluscicidal activity. Genome Announcements 1(2):e00175-12
  • Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Rosen B, Tar’an B, Millan T, Zhang X, Baek J, Ramsay, LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Sodelund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M-C, Thudi M, Gowda CLL, Singh HP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J and Cook D (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology 31(3):240-246
  • Sperschneider J, Gardiner DM, Taylor JM, Hane JK, Singh KB, Manners JM (2013) A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi. BMC Genomics 14(1):807
    Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon G, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ and Ciuffetti LM (2013) Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3-Genes Genomes Genetics 3(1):41-63
  • Syme RA, Hane JK, Friesen TL, Oliver RP (2013) Resequencing and comparative genomics of Stagonospora nodorum: Sectional gene absence and effector discovery. G3-Genes Genomes Genetics 3(6):959-969
  • Ipcho S, Hane J, Antoni E, Ahren D, Henrissat B, Friesen T, Solomon P, Oliver R (2012) Transcriptome analysis of Stagonospora nodorum: gene models, effectors, metabolism and pantothenate dispensability. Molecular Plant Pathology 13(6):531-545
  • Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S, Cozijnsen, AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, Kema GHJ, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachowiak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent M-H and Howlett BJ (2011) Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nature Communications 2:202
  • Hane JK, Rouxel T, Howlett BJ, Kema GHJ, Goodwin SB and Oliver RP (2011) A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biology 12(5):R45
  • Goodwin SB, Ben M’Barek S, Dhillon B, Wittenberg AHJ, Crane CF, Hane JK, Foster AJ, Van der Lee TAJ, Grimwood J, Aerts A, Antoniw J, Bailey A, Bluhm B, Bowler J, Bristow J, van der Burgt A, Canto-Canché B, Churchill ACL, Conde-Ferràez L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De Wit P, Donzelli B, van de Geest HC, van Ham RCHJ, Hammond-Kosack KE, Henrissat B, Kilian A, Kobayashi AK, Koopmann E, Kourmpetis Y, Kuzniar A, Lindquist E, Lombard V, Maliepaard C, Martins N, Mehrabi R, Nap JPH, Ponomarenko A, Rudd JJ, Salamov A, Schmutz J, Schouten H, Shapiro H, Stergiopoulos I, Torriani SFF, Tu H, de Vries RP, Waalwijk C, Ware SB, Wiebenga A, Zwiers L-H, Oliver RP, Grigoriev IV and Kema GHJ (2011) Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis. PLOS Genetics 7(6):e1002070
  • Gao LL, Hane J, Kamphuis L, Foley R, Shi BJ, Atkins C and Singh KB (2011) Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a Bacterial Artificial Chromosome (BAC) library and BAC-end sequencing. BMC Genomics 12(1):521
  • Ellwood SR, Liu ZH, Syme RA, Lai ZB, Hane JK, Keiper F, Moffat CS, Oliver RP and Friesen TL (2010) A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres. Genome Biology 11(11):R109
  • van de Wouw AP, Cozijnsen AJ, Hane JK, Brunner PC, McDonald BA, Oliver RP and Howlett BJ (2010) Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants. PLoS Pathogens 6(11):e1001180
  • Hane JK and Oliver RP (2010) In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. BMC Genomics 11(1):655
  • Antoni EA, Rybak K, Tucker MP, Hane JK, Solomon PS, Drenth A, Shankar M and Oliver RP (2010) Ubiquity of ToxA and absence of ToxB in Australian populations of Pyrenophora tritici-repentis. Australasian Plant Pathology 39(1):63-68
  • Bringans S, Hane JK, Casey T, Tan K-C, Lipscombe R, Solomon PS and Oliver RP (2009) Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum. BMC Bioinformatics 10(1):301
  • Solomon PS, Ipcho SVS, Hane JK, Tan KC and Oliver RP (2008) A quantitative PCR approach to determine gene copy number. Fungal Genetics Reports 55:5-8
  • Ellwood SR, Phan HTT, Jordan M, Hane JK, Torres AM, Avila CM, Cruz-Izquierdo S and Oliver RP (2008) Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris. BMC Genomics 9(1):380
  • Hane JK and Oliver RP (2008) RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences. BMC Bioinformatics 9(1):478
  • Hane JK, Lowe RGT, Solomon PS, Tan KC, Schoch CL, Spatafora, JW, Crous PW, Kodira C, Birren BW, Galagan JE, Torriani SFF, McDonald BA and Oliver RP (2007) Dothideomycete–plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. The Plant Cell 19(11):3347-3368
  • Phan HTT, Ellwood SR, Hane JK, Ford R, Materne M and Oliver RP (2007) Extensive macrosynteny between Medicago truncatula and Lens culinaris ssp. culinaris. Theoretical and Applied Genetics 114(3):549-558
  • Nelson MN, Phan HTT, Ellwood SR, Moolhuijzen PM, Hane JK, Williams A, O‘Lone CE, Fosu-Nyarko J, Scobie M, Cakir M, Jones MGK, Bellgard M, Ksiazkiewicz M, Wolko B, Barker S, Oliver RP and Cowling WA (2006) The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula. Theoretical and Applied Genetics 113(2):225-238

Book Chapters

  • Hane JK, Williams AH, Taranto AP, Solomon PS, Oliver RP (2015) Repeat-Induced Point Mutation: A Fungal-Specific, Endogenous Mutagenesis Process. In: Genetic Transformation Systems in Fungi Volume 2:55-68
  • Hane JK (2015) Calculating RIP Mutation in Fungal Genomes Using RIPCAL. In: Genetic Transformation Systems in Fungi Volume 2:69-78
  • Hane JK, Williams AH, Oliver RP (2011) Genomic and Comparative Analysis of the Class Dothideomycetes. In: The Mycota A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research Volume XIV:205-229
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Dr James Hane, Senior Research Fellow, Program Leader, CCDM Bioinformatics program, Centre for Crop & Disease Management